[gmx-users] NVT simulation and mdp file
teklebrh at ualberta.ca
teklebrh at ualberta.ca
Thu Mar 4 23:28:31 CET 2010
Hi Justin,
It does not work. I eliminated the hydrogen atoms and check the entire
.pdb file but could not solve the problem.
the modified PDB file.
REMARK This PDB file is created by CS Chem3D
REMARK
COMPND Tolene.pdb
HETATM 1 CB PHE 0 -1.158 0.001 0.000
CH2
HETATM 2 CG PHE 0 -1.158 -1.336 0.000 C
HETATM 3 CD1 PHE 0 -0.000 -2.004 0.000
CR1
HETATM 4 CD2 PHE 0 1.158 -1.336 0.000
CR1
HETATM 5 CE1 PHE 0 1.158 0.001 0.000
CR1
HETATM 6 CE2 PHE 0 -0.000 0.670 0.000
CR1
HETATM 7 CZ PHE 0 -0.000 2.167 0.000
CR1
END
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.rtp
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
WARNING: masses will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat
Entries in atommass.dat: 178
WARNING: vdwradii will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat
Entries in vdwradii.dat: 28
Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat
Entries in dgsolv.dat: 7
Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat
Entries in electroneg.dat: 71
Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat
Entries in elements.dat: 218
Reading Tolene.pbd.gro...
-------------------------------------------------------
Program pdb2gmx, VERSION 4.0.5
Source code file: futil.c, line: 330
File input/output error:
Tolene.pbd.gro
-------------------------------------------------------
"It's So Lonely When You Don't Even
Any comment on that.
Rob
Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>
>
> teklebrh at ualberta.ca wrote:
>> Dear Justin,
>>
>> It really help all the feedback you gave me and thank you for that,.
>>
>> I have one issues as well.
>>
>> I try to generate the topology file the way you recommend me using
>> the pdb2gro but failed to get both the topology and gromacs file.
>>
>> This is my Toluene file in pdb file
>>
>> REMARK This PDB file is created by CS Chem3D
>>
>> REMARK
>>
>> COMPND Tolene.pdb
>>
>> HETATM 1 CB PHE 0 -1.158 0.001 0.000
>> C
>>
>> HETATM 2 CG PHE 0 -1.158 -1.336 0.000
>> C
>>
>> HETATM 3 CD1 PHE 0 -0.000 -2.004 0.000
>> C
>>
>> HETATM 4 CD2 PHE 0 1.158 -1.336 0.000
>> C
>>
>> HETATM 5 CE1 PHE 0 1.158 0.001 0.000
>> C
>>
>> HETATM 6 CE2 PHE 0 -0.000 0.670 0.000
>> C
>>
>> HETATM 7 CZ PHE 0 -0.000 2.167 0.000
>> C
>>
>> HETATM 8 H16 PHE 0 -2.111 0.551 0.000
>> H
>>
>> HETATM 9 H17 PHE 0 -2.111 -1.886 0.000
>> H
>>
>> HETATM 10 H18 PHE 0 -0.000 -3.104 0.000
>> H
>>
>> HETATM 11 H19 PHE 0 2.110 -1.886 0.000
>> H
>>
>> HETATM 12 H20 PHE 0 2.110 0.551 0.000
>> H
>>
>> HETATM 13 H21 PHE 0 1.049 2.538 0.000
>> H
>>
>> HETATM 14 H22 PHE 0 -0.524 2.537 -0.909
>> H
>>
>> HETATM 15 H23 PHE 0 -0.525 2.537 0.909
>> H
>>
>> END
>>
>>
>> I run
>> pdb2gmx -ff G43a1 -f TOL.pdb -o TOL.gro -p TOL.top -missing
>>
>> but I go the following error.
>>
>> Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat
>> Entries in electroneg.dat: 71
>> Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat
>> Entries in elements.dat: 218
>> Reading YY.pdb...
>> Read 'Tolene.pdb', 15 atoms
>> Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat
>> 26 out of 26 lines of xlateat.dat converted succesfully
>> Analyzing pdb file
>> There are 1 chains and 0 blocks of water and 1 residues with 15 atoms
>>
>> chain #res #atoms
>> 1 ' ' 1 15
>>
>> All occupancy fields zero. This is probably not an X-Ray structure
>> Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.atp
>> Atomtype 1
>>
>>
>> I tried many times but could not get the topology file.
>>
>> Can you comment on this please.
>>
>
> What you've shown isn't an error. It reflects the fact that you
> don't even have occupancy values in this .pdb file. You will
> certainly have a nomenclature problem, though - your H atoms are not
> named according to what the .rtp file expects, so you'll either need
> to delete the H atoms and let pdb2gmx rebuild them from the .hdb
> entries, or use -ignh.
>
> -Justin
>
>> Rob
>>
>>
>> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>>
>>>
>>>
>>> teklebrh at ualberta.ca wrote:
>>>> Dear Gromacs Users,
>>>>
>>>> I have encountered the following issues while I was running my MD
>>>> simulation. Can anybody comment on what the meaning of these
>>>> notes are. Is there anything I could do to avoid them.
>>>>
>>>> NOTE 2 [file PAP.top, line unknown]:
>>>>
>>>> The largest charge group contains 12 atoms.
>>>>
>>>> Since atoms only see each other when the centers of geometry of the charge
>>>>
>>>> groups they belong to are within the cut-off distance, too large charge
>>>>
>>>> groups can lead to serious cut-off artifacts.
>>>>
>>>> For efficiency and accuracy, charge group should consist of a few atoms.
>>>>
>>>> For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
>>>>
>>>> My SOLVENT IS TOLUENE --- the PRODRG gave me a topology file with
>>>> only one group charge only.
>>>>
>>>
>>> That's almost certainly wrong. See, for instance, the PHE side
>>> chain in the relevant .rtp entry for a more reasonable charge
>>> group setup. If you're using PRODRG defaults, then the charges
>>> are probably unsatisfactory, as well.
>>>
>>> The rationale for the charge group size is summed up here:
>>>
>>> http://lists.gromacs.org/pipermail/gmx-users/2008-November/038153.html
>>>
>>>> NOTE 1 [file nvt.mdp, line unknown]:
>>>>
>>>> The Berendsen thermostat does not generate the correct kinetic energy
>>>>
>>>> distribution. You might want to consider using the V-rescale thermostat.
>>>>
>>>>
>>>
>>> See the literature about this one, as well as the numerous list
>>> archive discussions. For initial equilibration, a weak coupling
>>> scheme is probably fine, but you can also use V-rescale. Also of
>>> interest:
>>>
>>> http://www.gromacs.org/Documentation/Terminology/Thermostats
>>>
>>>> NOTE 3 [file aminoacids.dat, line 1]:
>>>>
>>>> The optimal PME mesh load for parallel simulations is below 0.5
>>>>
>>>> and for highly parallel simulations between 0.25 and 0.33,
>>>>
>>>> for higher performance, increase the cut-off and the PME grid spacing
>>>>
>>>
>>> This all depends on the size of your system, how much of the work
>>> is distributed between the real-space Coulombic interaction and PME.
>>>
>>>>
>>>> In addition to the above notes I have also some questions about
>>>> the NVT and NPT simulation.
>>>>
>>>> 1)I am using toluene as a solvent to simulate my polymer, do I
>>>> need to use the compressibility of toluene which is 9.2e-5 or
>>>> the default value 4.5e-5 1/bar.
>>>
>>> Well, 4.5e-5 corresponds to water, which you aren't using...
>>>
>>> For NVT, this won't matter since the box is fixed, but for NPT,
>>> the compressibility will affect the response of your system to
>>> pressure. The differences may be minimal, but if you know the
>>> right value, why accept a wrong one?
>>>
>>>> 2)What about the dielectric constant (the dielectric constant for
>>>> toluene is 2-2.4), but the default value is 80 ( I assume this is
>>>> for water- am I right).
>>>
>>> Yes, the default again assumes water as the solvent.
>>>
>>>> 3)Is always rvdw = 1.4 nm for GROMOS96. As a result I have to
>>>> increase my box size of the solute at the beginning to a min of
>>>> 2*1.4 =2.8 ( min image convection). Is this the right way to do!
>>>
>>> At an absolute minimum. Keep in mind that the box vectors will
>>> fluctuate under NPT, so if the box decreases even a little bit
>>> below 2.8, you will be violating the minimum image convention.
>>>
>>>> 4)I run an NVT simulation to equilibrate my system for 100 ps.
>>>> When I checked my simulation at the end (successfully completed)
>>>> I noticed that the shape of my simulation box looks CIRCULAR!
>>>> some how the rectangular shape looks distorted. What does this
>>>> tell! Do you guys think something is wrong in my simulation.
>>>
>>> This could be some visualization artifact, or the components of
>>> your system have condensed within the box. Without actually
>>> seeing it, it's hard to tell. If you post an image online
>>> (Photobucket, etc) then we might get a better sense of what's
>>> going on.
>>>
>>>> 5)I included the polar and aromatic hydrogens in my simulation (
>>>> ffG43a1.itp - GROMOS96.1 in PRODRG). Does these hydrogen
>>>> influence my result as the force field is a united atom force
>>>> field. Or How can I get rid of them if I want. With or without
>>>> the aromatic hydrogen gave good results ( besides lower
>>>> computational cost). Does Gromos96 model correctly
>>>> aromatic-Aromatic interaction.
>>>>
>>>
>>> Well, "correct" is a relative term for all force fields, but you
>>> need to follow the prescribed setup of the force field itself,
>>> otherwise you can throw it all away. If you lump the hydrogens
>>> into the ring carbons and have an uncharged ring, the result will
>>> be different than if you have the hydrogens there with a small
>>> charge on each C and H. Again, refer to the force field .rtp file
>>> for examples. You can also create a better toluene topology by
>>> renaming the residue in your coordinate file PHE and trick pdb2gmx:
>>>
>>> pdb2gmx -f toluene.pdb -missing
>>>
>>> Then change the mass of the CH2 group (which pdb2gmx thinks is a
>>> CB for PHE) to reflect a CH3 group. Make an .itp file out of the
>>> resulting .top by removing the unnecessary #includes, [system],
>>> and [molecule] directives. Then you don't have to worry about
>>> messing with PRODRG. I should note, as well, that this is about
>>> the only appropriate use of -missing I can think of at the moment
>>> (just for clarity in the archives; I usually warn against using
>>> -missing).
>>>
>>> -Justin
>>>
>>> --
>>> ========================================
>>>
>>> Justin A. Lemkul
>>> Ph.D. Candidate
>>> ICTAS Doctoral Scholar
>>> MILES-IGERT Trainee
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>> ========================================
>>> --
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>>>
>>
>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
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